Comparing the Mormon Wars (itself a misnomer) to Jihad or Crusade isn't quite accurate, though certain stages of armed Mormon violence were encouraged by their leaders using terms very similar to those used in holy wars. They were almost entirely defensive actions from the beginning. The history of the Mormons in America (at least until the statehood of Utah) can best be understood as a religiously extreme group struggling against violence perpetrated against them.

(Edit: As /u/AnOldHope rightly points out, contemporary sources DO compare Joseph Smith to Mohammed. Joseph Smith even compared himself to Mohammed. It is well worth exploring the history of this comparison.)

To understand this time period, you absolutely must understand the Second Great Awakening. The rise of the Mormon church was by no means unique at the time. There were countless people claiming to have powers of prophecy, preaching that the Second Coming was at hand, and starting utopian communities. Many were Restorationist movements, claiming that all existing churches had fallen away from the true teachings of Jesus Christ, and that their own churches would "restore" the true church. (Here's a Wikipedia link for a general understanding of this time; don't worry, primary sources are inbound: http://en.wikipedia.org/wiki/Second_Great_Awakening)

The neighbors of such communities were nervous about groups that claimed to answer to a power higher than the government of the United States and were led by religious zealots. Many Mormons also had strong economic influence, and they tended to do business among themselves, pushing out non-Mormons. The Mormons were also armed and pushed back against their enemies. It's worth noting the religious zeal and motivation expressed in the Zion's Camp movement to "reclaim Zion," their term for the "chosen city" to be founded around Independence, Missouri.

The Mormons were thought by some to be an armed religious cult. They were led by religious rather than secular authorities (the church were dubbed a "theodemocracy") who claimed to receive direct "revelation" from God. They were distrustful towards outsiders; for example, they adopted a practice called "whistling and whittling." If an outsider came to Nauvoo, Mormon men would happen to appear nearby him, moving ever closer while whittling wood with notably large knives and whistling loudly to drown out the outsider's attempts to talk. The message was clear. The Mormons adopted this practice as a means to protect themselves from violent outsiders; if they didn't know someone's business in Nauvoo, they would rightly be suspicious of that person's intentions.

Because of the powerful religious background of this time period, it's difficult to find unbiased and purely historical accounts about these events. These sources, while firsthand accounts, are certainly biased and must be treated as such:

A brief history of the Church of Christ of Latter-day Saints (commonly called Mormons) including an account of their doctrine and discipline; with the reasons of the author for leaving the church https://archive.org/details/briefhistoryofch00tayl

An extensive collection of newspaper accounts about the Mormons, collected by an LDS professor: http://www.sidneyrigdon.com/dbroadhu/artindex.htm

History of the Church of Jesus Christ of Latter-day Saints, Volume 1 The Mormon version of the events. https://archive.org/details/historyofchurcho01robe

Edit: I'm by no means an expert on the subject, and that's why I won't endeavor to suggest a more modern book to you that would give you a historical perspective. I thought I'd share a little I've come across in my research about the West, though.

Allow me to be a tad crass. You are trying to sell yourself to the various grad programs. This means being able to demonstrate your ability to perceive gaps in the field, your keen insights, and your ability to bring something new to the conversation. Ideally, you are moving the conversation along in new directions. Why should they invest in you? This means knowing the turns in Mormon historiography.

In 2009, J. Spencer Fluhman laid out his assessment of Mormon historiography in the Journal of Mormon History. Fluhman bemoaned scholars' obsession with early Mormon history, from roughly 1830-1890. Fluhman wanted scholars to focus on issues after Latter-day Saint Mormons abandoned polygamy, focusing instead on issues of the movement of Latter-day Saints from the fringes of society to putting forth legitimate political candidates in non-LDS strongholds and the movement of LDS Mormons to respectability. Scholars have yet to rise to Fluhman's challenge. (Jan Shipps dealt with many of these issues, but she has not plumbed the depths. Nevertheless, just three years later in 2012, Fluhman published his excellent work "A Peculiar People", which dealt exclusively with anti-Mormonism in the 1800s. You know, the same period he chided other scholars for focusing on.

Fluhman, however, should not be seen as an example of hypocrisy: "Do what I say, not what I do." There is still work to be done in the fields of 1800s Mormonism. Rather, what Fluhman highlights is that there is still important work to be done with regards to 1800s Mormonism, so long as one takes a fresh angle on the material. Fluhman's work is part of an establishing tradition that looks at anti-Mormonism to demonstrate its role in the shaping and formation of Mormonism and the coercive Protestant hegemony of the US. Other words, such as Mason's brilliant 2011 work The Mormon Menace. Mason departs from the established narrative of Mormonism that implicitly discussed northern regional concerns, and looks to see how Mormons encountered the south. Both Mason and Fluhman are a part of the recent historiographic turn that deals with religious intolerance in the US. Indeed, your interpretative lens will be what saves you from engaging in a trite argument that does not excite grad schools.

I will disagree with parts of what /u/kingconanisaid. The assumption that runs through kingconani's post is that you are writing from the vantage point of the Mormons, as she or he rightly reminds you that Mormons did not use the language of Jihad. However, how did the Protestants interpret the Mormon action? Did they see it as a form of holy war against their Protestant US? A constant trope used against the Mormons was to compare Joseph Smith to the false--in their view--prophet of Islam, Muhammad.. Taking this angle, how did the perpetrators of the Haun's Mill Massacre in 1838 understand their tactic? There is a great wealth of secondary literature that deals with the Mohammad/Joseph Smith issue. For me, this is an exciting angle to take.

If you do wish to continue to follow the Mormon Wars issue, then I would encourage you to not only understand the issues of the Second Great Awakening, but also issues of disestablishment. Some great current literature to help you frame this debate: David Sehat's The Myth of American Religious Freedom and Porterfield's Conceived in Doubt. Both nicely sum up what I mean when I speak of a coercive Protestant hegemony. I would also look at Fluhman's book to better understand anti-Mormonism that animated the wars.

Edit: You know what might be interesting? Taking Mason's work on the South and applying it to the regionally ambiguous Missouri in the 1830s. Did notions of southern honor animated Mormon antipathy?

Normally I'd hold silent and wait for someone with expertise to pipe in here. But seeing as this post is already in the negatives... How about emailing the librarians at BYU? Especially if there's a library on their campus specifically serving the history department. I think it's a fascinating topic you've got there. I've heard some stories, but don't have any scholarly resources to point you toward myself.

You should contact /u/AnOldHope. He has done research on Mormonism in the past.